Different output results between only used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz and used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz with other database

[yougulianren]

Dear,
I have used vep to annotate snv file based on T2T CHM13 V2.0. Firstly, I have only used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz, and the command line is :
vep --database 0 --dir_plugins /plugins --fasta [PATH]/hs1.fa --force_overwrite --gff [PATH]/chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz --input_file [PATH]/sample1.vcf.gz --output_file [PATH]/test.vep.CHM13.gff.vcf --symbol

The output results look like normally:

Then, I have used the next command to annotate:
vep -i /work/sample1.vcf.gz --fasta /ref/hs1.fa --gff chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz --symbol --o /outdir/test.vep.CHM13.vep.vcf --force_overwrite --custom file= Homo_sapiens-GCA_009914755.4-2022_10-gnomad.vcf.gz,short_name=gnomad,format=vcf,type=exact,coords=0,fields=AF%AF_oth%AF_ami%AF_sas%AF_fin%AF_fin%AF_eas%AF_amr%AF_afr%AF_mid%AF_asj%AF_nfe --custom file=Homo_sapiens-GCA_009914755.4-2022_10-dbSNP155.vcf.gz,short_name=dbSNP155,format=vcf,type=exact,coords=0,fields=ASS%AttemptedAlleles%AttemptedLocus%CLNACC%CLNDISDB%CLNDN%CLNHGVS%CLNORIGIN%CLNREVSTAT%CLNSIG%CLNVI%COMMON%DSS%FREQ%GENEINFO%GNO%INT%NSF%NSM%NSN%PM%PSEUDOGENEINFO%PUB%R3%R5%RS%ReverseComplementedAlleles%SAO%SSR%SYN%SwappedAlleles%U3%U5%VC%dbSNPBuildID --custom file=Homo_sapiens-GCA_009914755.4-2022_10-clinvar.vcf.gz,short_name=clinvar,format=vcf,type=exact,coords=0,fields=AF_ESP%AF_EXAC%AF_TGP%ALLELEID%CLNDN%CLNDNINCL%CLNDISDB%CLNDISDBINCL%CLNHGVS%CLNREVSTAT%CLNSIG%CLNSIGCONF%CLNSIGINCL%CLNVC%CLNVCSO%CLNVI%DBVARID%GENEINFO%MC%ORIGIN%SSR --custom file=homo_sapiens_gca009914755v4_110_VEP_GO_plugin.gff.gz,short_name=GO,format=gff,coords=0,fields=Ontology_term

There are no gene information in output file:

Is there any error in my second command?

[olaaustine]

Hi @yougulianren,
Hope this meets you well?
Please if possible can you share your input file and what version of VEP was used.
Thank you very much.
Ola

[yougulianren]

@olaaustine
Versions:
ensembl : 111.a6cc543
ensembl-funcgen : 111.5327cdd
ensembl-io : 111.dbba8d6
ensembl-variation : 111.d616b1e
ensembl-vep : 111.0

input file:
sample1.vcf.gz

[olaaustine]

Hi @yougulianren,
Thank you for sharing your input file.
Please can you share your GFF files also and the custom files used?
Thank you very much
Ola.

[yougulianren]

gff: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz

custom files :
https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/vcf/Homo_sapiens-GCA_009914755.4-2022_10-gnomad.vcf.gz
https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/vcf/Homo_sapiens-GCA_009914755.4-2022_10-dbSNP155.vcf.gz
https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/vcf/Homo_sapiens-GCA_009914755.4-2022_10-clinvar.vcf.gz
homo_sapiens_gca009914755v4_110_VEP_GO_plugin.gff.gz

[olaaustine]

Hi @yougulianren,
Thank you for your patience with this.
I have not been able to recreate the issue with your first output although I am using a different FASTA file from yours.
If possible can you share the fasta file used and please why do you have the --database 0 in the VEP command in the first command, if possible can you run the command with just --database
Hoping to hear from you soon.
Thank you very much
Ola.